MolNFT v1 · #186555 · protein
Cryo-EM structure of xenopus patched-1 in complex with GAS1 and sonic hedgehog
7RHQ: “Cryo-EM structure of xenopus patched-1 in complex with GAS1 and sonic hedgehog”. Electron microscopy, 6 ligands (CLR, Y01, PLM), 17 pockets (best druggability 0.89). MolNFT v1 #186555 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RHQ
- Type
- protein
- Length
- 1,305 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Patched-1; Sonic hedgehog protein N-product; Growth arrest-specific protein 1
- UniProt
- Q98SW6, Q15465, P54826
- Ligands
- CLR, Y01, PLM, NAG, CA, ZN
- Pockets
- 17 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Patched-1 | protein | 974 | 53% helix, 7% strand | Q98SW6 |
| C | Sonic hedgehog protein N-product | protein | 171 | 20% helix, 16% strand | Q15465 |
| G | Growth arrest-specific protein 1 | protein | 160 | 64% helix, 1% strand | P54826 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A, C, G
- Y01 · Cholesterol hemisuccinate · ligand · chains A, G
- PLM · Palmitic acid · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, G
- CA · Calcium ion · metal · 2 copies · chains C
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.89 | 0.90 | 105 | Y01 |
| 2 | 284 | 0.85 | 0.95 | 37 | PLM |
| 3 | 636 | 0.79 | 0.84 | 55 | CLR |
| 4 | 1035 | 0.76 | 0.78 | 85 | empty |
| 5 | 351 | 0.73 | 0.84 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1456 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 949 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 716 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 5 glycan, 1 covalent, 1 lipid (disulfide, N-glycosylation, covalent ligand, palmitoylation).
Compared structures
- 7RHQ · Cryo-EM structure of Xenopus Patched-1 in complex with GAS1 and Sonic Hedgehog · the same entry in another collection · chain A against A, TM-score 1.00
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain C against A, TM-score 0.87
- P54826 · AlphaFold monomer V2.0 prediction for growth arrest-specific protein 1 (P54826) · a predicted model of the same protein · chain G against A, TM-score 0.59
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q98SW6
- Every structure of UniProt Q15465
- Every structure of UniProt P54826
- Elsewhere: RCSB PDB 7RHQ · PDBe 7RHQ · UniProt Q98SW6 · UniProt Q15465 · UniProt P54826
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